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The 1999-2003 Lexus RX300 models have a common failure of the engine computer that causes the harsh shifting of the transmission. You need to get the computer (ECM - Engine Control Module) rebuilt or replaced before it causes permanent damage to the transmission. Even if the transmission is already ruined, the ECM will still need to be repaired. Most often, the transmission is fine though, and rebuilding the ECM will restore the smooth shifts that the Lexus should have. Circuit Board Medics can rebuild the ECM and reprogram it so that you only have to plug it back in when you get it back. See the link below: http://circuitboardmedics.com/1999-2003-lexus-rx300-hard-transmission-shifting-ecm-ecu-computer-repair/
If the transmission "brain" in modern cars senses problems it can keep the tranny from shifting. Usually leaves you in second gear as a safety and warning indication. I don't now if that year lexus had this ability but getting it checked on a diagnostic computer that read transmission codes should shed some light on your situation.
Flush the fluid every 30-45k miles. I work for lexus and they make solid cars and transmissions but some es300 transmissions from that year range fail (a very small percent) they do only replace transmissions. After the replacement the cars are fine, its not necessarily anything the owner did.Ive seen mixed results from shops that rebuild these transmissions as they don't do them everyday, those shops see alot more gm ford and chrysler vehicles and many of their models fail before 100k.